Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development

• Published in: The Plant journal : for cell and molecular biology 2022-02, Vol.109 (3), p.477-489
• Main Authors: Khan, Deirdre, Ziegler, Dylan J., Kalichuk, Jenna L., Hoi, Vanessa, Huynh, Nina, Hajihassani, Abolfazl, Parkin, Isobel A. P., Robinson, Stephen J., Belmonte, Mark F.
• Format: Article
• Language: English
• Subjects: Bias; Brassica; Brassica napus; Brassica napus - genetics; Brassica napus - growth & development; canola; Comparative analysis; Crops, Agricultural - genetics; Crops, Agricultural - growth & development; Embryos; Endosperm; Gene expression; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene regulation; Genes, Plant; Genome, Plant; Genomes; laser microdissection; Lasers; Networks; Phenotypes; plant development; Plant Development - genetics; Plant reproduction; polyploidy; Rape plants; RNA-mediated interference; seed; Seed coats; Seeds; Seeds - genetics; Seeds - growth & development; Target recognition; Transcription factors; Transcription Factors - genetics; transcriptomics
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15587

SUMMARY We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole‐genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive‐lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome‐specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser‐microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that ‐omics level approaches to studying gene regulation in B. napus can benefit from both broad and high‐resolution analyses. Significance Statement Global gene expression profiling and laser microdissection of the B. napus seed identifies subgenome bias and spatial distribution of biological processes and transcription factor networks.